The next morning, Arjin arrives at Dax's quarters early. A rather intimidating male alien named Trajok answers asking what he wants, but Jadzia interrupts wearing nothing but a towel. Jadzia and the alien exchange pleasantries while Arjin watches uncomfortably. The alien leaves and while Jadzia gets dressed, she asks Arjin to get her a black hole. The two talk briefly before heading to Ops, and Arjin feels like he can't say anything right to impress Jadzia.

When they arrive at Ops, O'Brien and Kira are hunting Cardassian voles. The voles are becoming a problem because they are chewing through wires. Jadzia jumps in to help them in their hunt and ends up stunning a vole and handing it to Arjin who again looks uncomfortable and has no idea what to do with it.

"Subspace seaweed" snagged on a runabout warp nacelle

Jadzia takes Arjin in the runaboutUSS Mekong to a trip through the wormhole and back. On the way, the two Trills discuss training, past experiences, and flight experience. Arjin had recently obtained his fifth level flight training, which shocked Jadzia because she only obtained her third level in her last year of training. Jadzia assures her first trill initiate that he doesn't have to impress her. During the flight, the runabout runs through a subspace interphase pocket. The Mekong's starboardnacelle snagged a piece of "subspace seaweed" and is no longer functioning.

Meanwhile, O'Brien has come up with a directional sonic generator which can produce a sound at a frequency uncomfortable to the vole's ears and drive them out of hiding. Quark bursts into Ops carrying a dead vole that had run across a dabo table and demands they take care of the vermin problem. When O'Brien tries to demonstrate the sonic generator to Quark to show they are working on it, Quark falls to the ground screaming–the sonic generator works, at least on Ferengi. Jadzia and Arjin return to the station, and Jadzia wants to study this "subspace seaweed" further. She asks O'Brien to setup a containment chamber in the science lab, and O'Brien informs her it'll take a while.

While waiting, Jadzia takes Arjin to a Klingon restaurant on the Promenade where they discuss his past and eat racht. Arjin is less than thrilled with his Klingon meal, and reveals he's only in the initiate program because it was his father's dying wish and has no plans for the future. Back in Ops, O'Brien is getting desperate to handle this vole problem and contacts Cardassia looking for a solution. They provide no solution and "kindly" remind O'Brien that the vole mating season is fast approaching.

After dinner, Jadzia and Arjin part ways and Jadzia heads to Ops to talk to Benjamin Sisko about the "subspace seaweed" and Arjin. Jadzia admits she doesn't see Arjin being much of a host to a symbiont, but doesn't feel it's her place to confront him about it as it's very clear in the guidelines as to what she's supposed to do. Sisko disagrees and reminds Jadzia of the things Curzon Dax did to her.

In the science lab, a pair of voles manage to take down the security field that was surrounding the subspace sample. O'Brien has discovered the voles have eaten through the security fields energy lines, and Sisko tells him it's time to take the phasers off stun–to better handle the vole problem. Jadzia and Arjin continue their analysis on the sample, but Jadzia's attitude toward Arjin has changed–she's become more harsh and critical and accuses him of telling her what she wants to hear. Arjin feels betrayed because of their conversation in the runabout earlier, and begins to insult Jadzia, saying she is far below the standards of a host. He leaves the science lab and heads to Quark's to "drown himself" in synthehol. Quark has a disheartening talk with Arjin, explaining how he once missed his big opportunity and never recovered and welcomed Arjin to "the club".

Hull breach on DS9 on level 22 section 14

Jadzia has discovered the subspace sample is highly structured and doesn't conform to any physical laws. Further analysis reveals the electromagnetic flux are high plasma concentrations in a rapidly expanding mass. The mass is expanding in a very specific way that the computer recognized as the expansion patterns of a universe. Their "subspace seaweed" is actually a protouniverse in its early stages of formation. As it grows, it will displace their own universe. Returning it to the wormhole could prove devastating to the whole system if it came in contact with any of the wormhole's verteron nodes, and not doing anything would be just as bad. They decide to try to contain it using the universe's own feedback pressure to create an implosive wave destroying the protouniverse–and the science lab–in the process.

Jadzia continues to study the protouniverse, and discovers local entropy readings in the protouniverse have decreased 12% in the last hour. This shows indications of life in the protouniverse and these readings have been confirmed by the computer. They agree to cancel the containment field and let the protouniverse expand and destroy level 22 section 14 of the station, causing multiple hull breaches. Kira can't understand why they won't destroy the protouniverse, comparing it to stepping on ants to which Odo replies, "I don't step on ants, Major." When Kira presses them for another solution, Sisko says he'll have a decision in an hour.

Arjin avoiding verteron nodes in the wormhole

While thinking things over, Sisko drops by his quarters to visit Jake. While talking, Sisko finds out Jake is in love with a dabo girl named Mardah–the one Jake has been tutoring in entomology. Jake asks if she can come over for dinner tonight, and Sisko says not tonight but soon, he does want to meet her after all. Jadzia and Arjin are in Quark's talking more about the initiate program. Arjin is convinced it's over, but Jadzia says otherwise and explains her past and how she changed after meeting Curzon Dax. Sisko interrupts the two saying he's decided to take the protouniverse back through the wormhole. After preparing a containment field aboard the runabout that will block out the verteron node radiation, the protouniverse is beamed over and the journey through the wormhole begins.

While traveling through the wormhole, the containment field slowly starts to collapse. Every time they pass through a verteron node, the field gets weaker. They bring the runabout to a stop and decide to let the containment field fail and fly the runabout through the wormhole without touching any verteron nodes. This type of precision flying has never been done before, and Arjin is reluctant to try. Jadzia convinces him that he can do it, and he manages to get them to the Gamma Quadrant safely so they can return the protouniverse to where they found it. Jadzia tells Arjin this will look very good on his initiate record.

After the mission, Arjin apologizes to Jadzia for the things he said. Jadzia says she wouldn't recommend the process of being joined with a symbiont for everyone, but with time, she might recommend it for Arjin–when he's ready.

"You haven't touched your racht."
"No, I have. It's interesting."
"No, you've moved it around your plate to make it look like you've touched it."
"I didn't have to move it. It moved itself."

- Dax and Arjin

"Take those phasers off stun, Chief. No more Mister Nice Guy."

- Benjamin Sisko

"I should have known this. I should have realized this. You're Dax! Standards for Trill hosts? That is really incredible coming from you. I have never seen any host in my life who is so far below those standards as you are, ma'am! No wonder Curzon Dax tried to terminate your training."

- Arjin to Jadzia Dax, after feeling betrayed

"There isn't a problem in the world that can't be fixed by the right holosuite program."

"Personal log. Supplemental. One hour. One hour to make a decision that could mean the life or death of a civilization. Or the end to our own. My mind keeps going back to the Borg... how I despised their... indifference as they tried to exterminate us. And I have to ask myself... would I be any different if I destroyed another universe to preserve my own?"

In writer Jim Trombetta's first draft of the teleplay, the A story was the protouniverse story, with Dax's storyline in secondary position. Michael Piller rewrote the episode to place the Trill storyline as the primary plot. Trombetta felt that this decision robbed the episode of its emotional balance and that the ethical problem of the protouniverse story is no longer felt on an emotional level. (Star Trek: Deep Space Nine Companion)

After "Shadowplay", this is the second A-B-C (three-story) episode in a row. Michael Piller commented "The problem with the script was always that nobody could find the balance between the three stories and nobody could find the relationship between the two characters". (The Deep Space Log Book: A Second Season Companion, p 37)

Terry Farrell says of Dax in this episode, "Everything she does in the beginning is an attempt to get Arjin to react to her, to shake him out of his behavior. Because somebody who's really mature enough to be a host would have handled that treatment differently than Arjin did." (Star Trek: Deep Space Nine Companion)

This episode marks the second and final appearance of the Klingon chef played by Ron Taylor. He previously appeared in the episode "Melora".

Richard Poe makes his first appearance in this episode. Although the script only refers to his character as "Cardassian Officer" and production sources credit him only as "Cardassian", it is apparent that this character became GulEvek, as in "Tribunal", Evek tells Miles O'Brien that they have spoken before.

The chess game played between Sisko and Dax in this episode is recognizable as the famous game D. Byrne vs R. Fischer, 1956 (known as the game of the century). The moves shown on screen are roughly moves 14 to 18.